As I mentioned in my first post, its for precisely locating the part on a board with no fiducials (ie: single sided copper clad that i've cut up on the bandsaw) and which have features very close to the edge (such as edge connectors), or when your Y distance is very close to where the clamps are (don't want to clash with them!)
Arrow keys would be perfect for fine positioning, but the mouse is still faster for coarse adjustment.
From a software perspective having ctrl + drag as you mention should be a fairly simple change, as you'd just ignore the move on the axes with the smaller units.
I have another post asking for the outline speed to be adjustable, as well as the height. At the moment I really can't tell just how well centred I am on the substrate. For the boards with RF connectors on the edges I'm getting to the height mapping step and seeing which side the probe falls of the board, going back and adjusting position, reprobing, rinse and repeat until both sides get probed on the board. I have features within 0.2mm of the edge of the board on both sides... so alignment counts